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All sources NASA NTRS DOE OSTI

DOE OSTI2020

ADEPT: a domain independent sequence alignment strategy for gpu architectures

Bioinformatic workflows frequently make use of automated genome assembly and protein clustering tools. At the core of most of these tools, a significant portion of execution time is spent in determining optimal local alignment between two sequences. This task is performed with the Smith-Waterman algorithm, which is a dynamic programming based method. With the advent of modern sequencing technologies and increasing size of both genome and protein databases, a need for faster Smith-Waterman implementations has emerged. Multiple SIMD strategies for the Smith-Waterman algorithm are available for CPUs. However, with the move of HPC facilities towards accelerator based architectures, a need for an efficient GPU accelerated strategy has emerged. Existing GPU based strategies have either been optimized for a specific type of characters (Nucleotides or Amino Acids) or for only a handful of application use-cases. In this paper, we present ADEPT, a new sequence alignment strategy for GPU architectures that is domain independent, supporting alignment of sequences from both genomes and proteins. Our proposed strategy uses GPU specific optimizations that do not rely on the nature of sequence. We demonstrate the feasibility of this strategy by implementing the Smith-Waterman algorithm and comparing it to similar CPU strategies as well as the fastest known GPU methods for each domain. ADEPT’s driver enables it to scale across multiple GPUs and allows easy integration into software pipelines which utilize large scale computational systems. We have shown that the ADEPT based Smith-Waterman algorithm demonstrates a peak performance of 360 GCUPS and 497 GCUPs for protein based and DNA based datasets respectively on a single GPU node (8 GPUs) of the Cori Supercomputer. Overall ADEPT shows 10x faster performance in a node-to-node comparison against a corresponding SIMD CPU implementation. ADEPT demonstrates a performance that is either comparable or better than existing GPU strategies. We demonstrated the efficacy of ADEPT in supporting existing bionformatics software pipelines by integrating ADEPT in MetaHipMer a high-performance denovo metagenome assembler and PASTIS a high-performance protein similarity graph construction pipeline. Our results show 10% and 30% boost of performance in MetaHipMer and PASTIS respectively.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS1993

System For Retrieving Reusable Software

Encyclopedia of Software Components (ESC) is information-retrieval system of computer hardware and software providing access to generic reusable software tools and parts. Core of ESC is central tool base, which is repository of reusable software. It receives queries and submissions from user through local browser subsystem and receives authorized updates from maintenance subsystem. Sends retrievals to local browser subsystem and user's submissions to maintenance subsystem. Future versions will provide for advanced media, including voice and video, and will link system to database-management system. Programmers will not only retrieve software, but also modify, execute, and cross-link with other software.

Van Warren, Lloyd↗

NASA NTRS2006

Deep impact sequence planning using multi-mission adaptable planning tools with integrated spacecraft models

The Deep Impact mission was ambitious and challenging. JPL's well proven, easily adaptable multi-mission sequence planning tools combined with integrated spacecraft subsystem models enabled a small operations team to develop, validate, and execute extremely complex sequence-based activities within very short development times. This paper focuses on the core planning tool used in the mission, APGEN. It shows how the multi-mission design and adaptability of APGEN made it possible to model spacecraft subsystems as well as ground assets throughout the lifecycle of the Deep Impact project, starting with models of initial, high-level mission objectives, and culminating in detailed predictions of spacecraft behavior during mission-critical activities.

Seybold, Calina C.↗

DOE OSTI2021

Secondary porosity prediction in complex carbonate reefs using 3D CT scan image analysis and machine learning

Development and preservation of carbonate porosity and permeability are critical to characterizing reservoirs. However, secondary porosity, such as vugs and fractures, are difficult to identify and require collection of expensive wireline tools or core sampling. Wireline logs and cores have traditionally been used to identify the presence of secondary porosity but fail to quantify the contribution to total reservoir porosity. Additionally, advanced wireline logs and core are not readily available for most wells. Dual energy CT scans were collected on whole core from the A-1 Carbonate and Brown Niagaran formations drawn from six wells in northern Michigan. 3D analysis techniques were applied to identify and isolate secondary porosity features. A series of machine learning and data analytics techniques were applied to the dataset to predict secondary porosity features on basic wireline logs. The predictive model successfully predicted secondary porosity with high confidence.

02 PETROLEUM↗

DOE OSTI2023

Ensuring thermodynamic consistency with invertible coarse-graining

Coarse-grained models are a core computational tool in theoretical chemistry and biophysics. A judicious choice of a coarse-grained model can yield physical insights by isolating the essential degrees of freedom that dictate the thermodynamic properties of a complex, condensed-phase system. The reduced complexity of the model typically leads to lower computational costs and more efficient sampling compared with atomistic models. Designing “good” coarse-grained models is an art. Generally, the mapping from fine-grained configurations to coarse-grained configurations itself is not optimized in any way; instead, the energy function associated with the mapped configurations is. In this work, we explore the consequences of optimizing the coarse-grained representation alongside its potential energy function. We use a graph machine learning framework to embed atomic configurations into a low-dimensional space to produce efficient representations of the original molecular system. Because the representation we obtain is no longer directly interpretable as a real-space representation of the atomic coordinates, we also introduce an inversion process and an associated thermodynamic consistency relation that allows us to rigorously sample fine-grained configurations conditioned on the coarse-grained sampling. We illustrate that this technique is robust, recovering the first two moments of the distribution of several observables in proteins such as chignolin and alanine dipeptide.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2024

Development of Two-Step Method for Fast Chloride MSR Neutronics

This work presents neutronics models of a small and large fast-spectrum molten chloride-salt reactor. The models are similar to designs being pursued by industry, and they may serve as generic preconceptual and simplified neutronics models that provide information for decision making in licensing-related areas. Here, the two models were created using Serpent, a Monte Carlo neutron transport code, and Moltres, a neutron diffusion core simulator tool. Specifically, this study focused on exploring the applicability of diffusion theory to fast molten salt reactor (MSR) models, the capabilities of an open-source, MSR-oriented simulation tool (Moltres), and optimal energy-group structures.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

DOE OSTI2022

Development and Demonstration of a Risk-Informed Approach to the Regulatory Required Fuel Reload Safety Analysis

The United States (U.S.) nuclear industry is facing a strong challenge to maintain regulatory-required levels of safety while ensuring economic competitiveness to stay in business. Safety remains a key parameter for all aspects related to the operation of light water reactor (LWR) nuclear power plants (NPPs) and can be achieved more economically by using a risk-informed ecosystem such as that being developed by the Risk-Informed Systems Analysis (RISA) Pathway under the U.S. Department of Energy (DOE) Light Water Reactor Sustainability (LWRS) Program. The LWRS Program is promoting a wide range of research and development (R&D) activities with the goal to maximize both the safety and economically efficient performance of NPPs through improved scientific understanding, especially given that many plants are considering second license renewal. The RISA Pathway has two main goals: (1) the deployment of methodologies and technologies that enable better representation of safety margins and the factors that contribute to cost and safety; and (2) the development of advanced applications that enable cost-effective plant operation. The plant reload optimization framework development project aims to build an artificial intelligence, i.e., Genetic Algorithm (GA), based reactor core designing tool taking into account reactor safety and fuel performance analyses.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

NASA NTRS2003

Mission interactive scenarion studio for autonomous spacecraft

We propose building a Studio enabling the use of diverse existing mission activity and scenario patterns, the creation of new ones, and the modeling of their effects using existing modeling tools. The core of the Studio is a component-based Type Library, which captures years of mission adaptation patterns in various forms. The Studio works as a content server to capture the developed adaptation knowledge for reuse and provides bridging into different mission uplink implementations, including the Mission Data System [l] (MDS) state/goal machinery. Various activities can be coordinated, controlled, and reused through the Studio's component interface to establish and model a mission scenario. A special component Factory mechanism will be in place to facilitate the adaptation of projects into the Studio. The architecture of the Studio reflects and enforces a division of knowledge and actions into three parts: Model, Controller, Viewer. The Model contains information about (a proposed version of) the spacecraft and mission. The Controller contains logic for constructing scenarios of mission activities. The information in the Model and Controller is principally in the form of reusable patterns. A Viewer can be a simple or complex software system. For example, Apgen [2,3] is one possible viewer, MDS is another. A 3-tiered infrastructure is used for the Studio, reflecting the Model, Controller, Viewer architecture [4,5]. The Studio is useful in pre-phase A of a project by enabling spacecraft design options to be played against desired mission scenarios. In later design phases of a project, the construction and modeling of more detailed scenarios is supported by the Studio.

autonomous spacecraft↗

NASA NTRS2007

NASA Tech Briefs, March 2007

Topics include: Advanced Systems for Monitoring Underwater Sounds; Wireless Data-Acquisition System for Testing Rocket Engines; Processing Raw HST Data With Up-to-Date Calibration Data; Mobile Collection and Automated Interpretation of EEG Data; System for Secure Integration of Aviation Data; Servomotor and Controller Having Large Dynamic Range; Digital Multicasting of Multiple Audio Streams; Translator for Optimizing Fluid-Handling Components; AIRSAR Web-Based Data Processing; Pattern Matcher for Trees Constructed From Lists; Reducing a Knowledge-Base Search Space When Data Are Missing; Ground-Based Correction of Remote-Sensing Spectral Imagery; State-Chart Autocoder; Pointing History Engine for the Spitzer Space Telescope; Low-Friction, High-Stiffness Joint for Uniaxial Load Cell; Magnet-Based System for Docking of Miniature Spacecraft; Electromechanically Actuated Valve for Controlling Flow Rate; Plumbing Fixture for a Microfluidic Cartridge; Camera Mount for a Head-Up Display; Core-Cutoff Tool; Recirculation of Laser Power in an Atomic Fountain; Simplified Generation of High-Angular-Momentum Light Beams; Imaging Spectrometer on a Chip; Interferometric Quantum-Nondemolition Single-Photon Detectors; Ring-Down Spectroscopy for Characterizing a CW Raman Laser; Complex Type-II Interband Cascade MQW Photodetectors; Single-Point Access to Data Distributed on Many Processors; Estimating Dust and Water Ice Content of the Martian Atmosphere From THEMIS Data; Computing a Stability Spectrum by Use of the HHT; Theoretical Studies of Routes to Synthesis of Tetrahedral N4; Estimation Filter for Alignment of the Spitzer Space Telescope; Antenna for Measuring Electric Fields Within the Inner Heliosphere; Improved High-Voltage Gas Isolator for Ion Thruster; and Hybrid Mobile Communication Networks for Planetary Exploration.

Source record↗

NASA NTRS2007

The Mock LISA Data Challenges: History, Status, Prospects

This slide presentation reviews the importance for the Mock LISA Data Challenges (MLDC). Laser Interferometer Space Antenna (LISA) is a gravitational wave (GW) observatory that will return data such that data analysis is integral to the measurement concept. Further rationale of the MLDC are to kickstart the development of a LISA data-analysis computational infrastructure, and to encourage, track, and compare progress in LISA data-analysis development in the open community. The MLDCs is a coordinated, voluntary effort in GW community, that will periodically issue datasets with synthetic noise and GW signals from sources of undisclosed parameters; increasing difficulty. The challenge participants return parameter estimates and descriptions of search methods. Some of the challenges and the resultant entries are reviewed. The aim is to show that LISA data analysis is possible, and to develop new techniques, using multiple international teams for the development of LISA core analysis tools

data analysis↗

DOE OSTI2024

Impact of Reordering on the LU Factorization Performance of Bordered Block-Diagonal Sparse Matrix

Power engineers rely on computer-based simulation tools to assess grid performance and ensure security. At the core of these tools are solvers for sparse linear equations. When transformed into a bordered block-diagonal (BBD) structure, part of the sparse linear equation solving can be parallelized. This work focuses on using the Schur-complement-based method for LU factorization on BBD matrices, specifically, Jacobian matrices from large-scale systems. Our findings show that the natural ordering method outperforms the default ordering method in computational performance for each block of the BBD matrix. This observation is validated using synthetic 25k-bus and 70k-bus cases, showing a speedup of up to 38% when using natural ordering without permutation. Additionally, the impact of the number of partitions is studied, and the result shows that computational performance improves with more, smaller partitions in the BBD matrices.

BBD matrix↗

NASA NTRS2016

Tracking Blade Tip Vortices for Numerical Flow Simulations of Hovering Rotorcraft

Blade tip vortices generated by a helicopter rotor blade are a major source of rotor noise and airframe vibration. This occurs when a vortex passes closely by, and interacts with, a rotor blade. The accurate prediction of Blade Vortex Interaction (BVI) continues to be a challenge for Computational Fluid Dynamics (CFD). Though considerable research has been devoted to BVI noise reduction and experimental techniques for measuring the blade tip vortices in a wind tunnel, there are only a handful of post-processing tools available for extracting vortex core lines from CFD simulation data. In order to calculate the vortex core radius, most of these tools require the user to manually select a vortex core to perform the calculation. Furthermore, none of them provide the capability to track the growth of a vortex core, which is a measure of how quickly the vortex diffuses over time. This paper introduces an automated approach for tracking the core growth of a blade tip vortex from CFD simulations of rotorcraft in hover. The proposed approach offers an effective method for the quantification and visualization of blade tip vortices in helicopter rotor wakes. Keywords: vortex core, feature extraction, CFD, numerical flow visualization

Numerical↗

DOE OSTI2024

RELAP5-3D in the OECD-NEA HTGR Thermal Hydraulics Benchmark

The OECD-NEA HTGR Thermal Hydraulics benchmark uses data from the High Temperature Test Facility for a series of code-to-code and code-to-data exercises aimed at improving the state of knowledge on existing thermal hydraulics modeling and simulation tools for prismatic HTGR applications. This benchmark includes problems representing hot gas mixing in the lower plenum, the depressurized conduction cooldown accident and the pressurized conduction cooldown accident. This presentation discusses the benchmark and RELAP5-3D's role in that benchmark, including as a tool for predicting behavior in the core and as a tool for providing boundary conditions to computational fluid dynamics analysis in the lower plenum.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

DOE OSTI2024

IDAES-PSE 2.7.0 Release

The Institute for the Design of Advanced Energy Systems (IDAES) Integrated Platform is a versatile computational environment offering extensive process systems engineering (PSE) capabilities for optimizing the design and operation of complex, interacting technologies and systems. IDAES enables users to efficiently search vast, complex design spaces to discover the lowest cost solutions while supporting the full process modeling lifecycle, from conceptual design to dynamic optimization and control. The extensible, open platform empowers users to create models of novel processes and rapidly develop custom analyses, workflows, and end-user applications. IDAES-PSE 2.7.0 Release Highlights New features: AutoScaler and CustomScalerBase classes: Such tools are the core of the new scaling framework being implemented in IDAES. Wider adoption of scaling tools among users will result in quicker and more robust model solutions. Scaler for equilibrium reactor and saponification properties: These scaler models are examples to follow for how to use the new scaling tools. ONNX Surrogate support from Optimization & Machine Learning Toolkit (OMLT): ONNX is an open standard format to save and load ML/AI models that is widely supported by all major frameworks. This capability makes it easier for IDAES users to create surrogate models and use them without having to support each framework individually. 1D Membrane Model for CO2 Capture and Utilization: Supports ongoing efforts for modeling and optimizing polymer membrane processes for CO2 capture and conversion into formic acid. StreamScaler unit model: Unrelated to the CustomScalerBase, this unit model allows a stream’s extensive variables to be scaled by a fixed factor. This allows streams being processed by multiple units in parallel to be scaled down to unit scale and scaled back up to process scale. Bug fixes or improvements: Scaling, EoS, Diagnostics tool, Modular Properties, tests & documentation Deprecations: Old Cubic EoS

AS↗

NASA NTRS2012

Rotary Percussive Sample Acquisition Tool

As part of a potential Mars Sample Return campaign NASA is studying a sample caching mission to Mars, with a possible 2018 launch opportunity. As such, a Sample Acquisition Tool (SAT) has been developed in support of the Integrated Mars Sample Acquisition and Handling (IMSAH) architecture as it relates to the proposed Mars Sample Return (MSR) campaign. The tool allows for core generation and capture directly into a sample tube. In doing so, the sample tube becomes the fundamental handling element within the IMSAH sample chain reducing the risk associated with sample contamination as well as the need to handle a sample of unknown geometry. The tool's functionality was verified utilizing a proposed rock test suite that encompasses a series of rock types that have been utilized in the past to qualify Martian surface sampling hardware. The corresponding results have shown the tool can effectively generate, fracture, and capture rock cores while maintaining torque margins of no less than 50% with an average power consumption of no greater than 90W and a tool mass of less than 6kg.

Sample Acquisition and Caching (SAC)↗

NASA NTRS2009

Proof of Concept Study of Trade Space Configuration Tool for Spacecraft Design

Spacecraft design is a very difficult and time consuming process because requirements and criteria are often changed or modified as the design is refined. Accounting for these adjustments in the design constraints plays a significant role in furthering the overall progress. There are numerous aspects and variables that hold significant influence on various characteristics of the design. This can be especially frustrating when attempting to conduct rapid trade space analysis on system configurations. Currently, the data and designs considered for trade space evaluations can only be displayed by using the traditional interfaces of Excel spreadsheets or CAD (Computer Aided Design) models. While helpful, these methods of analyzing the data from a systems engineering approach can be rather complicated and overwhelming. As a result, a proof of concept was conducted on a dynamic data visualization software called Thinkmap SDK (Software Developer Kit) to allow for better organization and understanding of the relationships between the various aspects that make up an entire design. The Orion Crew Module Aft Bay Subsystem was used as the test case for this study because the design and layout of many of the subsystem components will be significant in ensuring the overall center of gravity of the capsule is correct. A simplified model of this subsystem was created and programmed using Thinkmap SDK to create a preliminary prototype application of a Trade Space Configuration Tool. The completed application ensures that the core requirements for the Tool can be met. Further development is strongly suggested to produce a full prototype application to allow final evaluations and recommendations of the software capabilities.

Glidden, Geoffrey L.↗

DOE OSTI2023

FY23 Status Report on MOOSE-Based Approaches to Modeling Core Bowing in Fast Reactors

Under the U.S. Department of Energy Office of Nuclear Energy’s Advanced Modeling and Simulation (NEAMS) Program, an integrated multiphysics approach is being developed to model the core bowing phenomena important to liquid metal-cooled fast reactors. Core bowing is an important passive safety mechanism whereby increased power (which leads to temperature and flux gradients) influences the core to bow into less reactive configurations when the restraint system is properly designed. The phenomenon includes a complex interplay of radiation transport, duct temperature calculations involving fluid flow and heat transfer, and thermo-mechanical responses to the induced temperature and flux gradients. Structural material properties are also important to determining inelastic response to longer term flux gradients which cause irradiation creep and swelling. While core bowing provides a strong negative reactivity feedback when the restraint system is designed properly, it also results in additional forces between assemblies which increase the loads required to extricate them during refueling or control rod movement. Therefore, the restraint system must be designed with these tradeoffs in mind. The first stage of the work, which commenced in FY21 and continues through FY23, assesses thermo-mechanical modeling tools for producing core bowing predictions consistent with conventional tools. The Multiphysics Object Oriented Simulation Environment (MOOSE) Tensor Mechanics and Contact Modules are employed. This status report describes work on additional thermo-mechanical benchmark verification problems with increased complexity from the examples demonstrated in FY21 and FY22. Several benchmark verification examples were selected from the IAEA verification and validation report with increased number of ducts and more complex contact interaction behavior. These examples involve a full symmetric sector with restraint rings at multiple load pad locations to simulate a limited free-bow restraint system concept, as well as irradiation induced swelling and creep effects in a sector. In addition, improvements to the contact module sideset assignment were assessed and compared with previous MOOSE results to verify the contact behavior. The MOOSE-based results were compared to IAEA benchmark participants’ results. In every case, the MOOSE results agreed with other simulations results for estimating bowing behavior, providing additional verification basis of the tools for this particular physics application. Estimation of contact forces were mostly in agreement, with a few outlier results. A plan was suggested for dealing with the discrepancies with estimating contact force values. In addition, a 1-way coupling demonstration was performed using subchannel analysis code Pronghorn-SC and MOOSE on an ABR-1000-design sodium-cooled fast reactor assembly to evaluate coolant and duct wall temperatures.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

NASA NTRS2018

Collaborative Systems Engineering in the Ascent Abort-2 Crew Module/Separation Ring Project

Generally speaking, systems engineering (SE) tool-sets face a dilemma balancing power and accessibility. High-powered SE tools (MagicDraw, Cradle, Core, etc.) tend to be specialized and are available only to highly trained Systems Engineers, and/or through the use of a 'back room' developer team making the output products available to the broader team. On the other hand, highly accessible tools (MS Word, Excel, etc.) do not have the power to implement SE in a rigorous manner. NASA has to test all aspects of the new human-rated Orion Multi-Purpose Crew Vehicle spacecraft prior to its first crewed mission. The test program includes uncrewed launch abort flight tests to demonstrate the capability to save the crew in the event that a launch failure occurs. Orion's second abort flight test will be a low-altitude flight test known as "Ascent Abort 2 (AA-2)." This test is currently scheduled to be carried out at Cape Canaveral Air Force Station's Space Launch Complex 46 (SLC-46) in Florida in 2019. NASA's in-house AA-2 Crew Module and Separation Ring (CSR) Team is producing the crew module and separation ring. Operating jointly as both an Advanced Exploration Systems (AES) Project and an Orion Project, the CSR project charter includes development of innovative, streamlined and generally more efficient practices for creation of flight hardware and software. One result of this tasking has been development of a collaborative and data-centric systems engineering environment within the team's shared web environment (Microsoft SharePoint). Through the use of built-in, 'out of the box capabilities' present in MS SharePoint, the CSR Systems Engineering team has created (with some limited developer support) a data-centric architecture for the project's SE implementation, including functional and interface analysis, requirements development and management, risk management, verification planning and management, test results, and end item management. Data elements are linked between data structures so as to define and control relationships between item types, link requirements to parents and children, and link tests to the requirements that they verify. The overall project team integration is increased by also linking SE content to project management content over the project life cycle, including team communication, action items, configuration management, decisional and meeting materials, and life cycle reviews. This presentation will provide an overview of the collaborative SE environment, showing how it provides the power for a number of SE tasks while still providing the accessibility and transparency to allow the full project team to collaborate and succeed. Given the project phase, we'll be able to present a nearly full lifecycle discussion, from concept through verification and approaching delivery.

Systems Engineering environments↗